ReviewNature protocols2022
Optimization of metabolomic data processing using NOREVA.
Review in Nature protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
40 citing papers in PubMed.
- Reimagining Lignin Valorization: Synthetic Biology-Enabled Sustainable Aromatic Carbon Biomanufacturing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Integrated transcriptomic and metabolomic analyses reveal light-quality-dependent regulation of specialized metabolism in Pseudostellaria heterophylla.BMC genomics · 2026Article
- Navigating the data processing for cytometry-based single-cell proteomics.Nature protocols · 2026Review
- Deciphering cross-cohort metabolic signatures of immune responses and their implications for disease pathogenesis.Molecular systems biology · 2025Article
- Article
- A novel prognostic risk score associated with resistance to docetaxel chemotherapy for predicting biochemical recurrence-free survival in patients with prostate cancer.Discover oncology · 2025Article
- LocPro: A deep learning-based prediction of protein subcellular localization for promoting multi-directional pharmaceutical research.Journal of pharmaceutical analysis · 2025Article
- Spatially Resolved Multiomics: Data Analysis from Monoomics to Multiomics.BME frontiers · 2025Review
- The mitochondrial dicarboxylate carrier mediates in vivo hepatic gluconeogenesis.bioRxiv : the preprint server for biology · 2024Article
- Antiprotozoal peptide prediction using machine learning with effective feature selection techniques.Heliyon · 2024Article
- SPTLC3 Is Essential for Complex I Activity and Contributes to Ischemic Cardiomyopathy.Circulation · 2024Article
- A diverse proteome is present and enzymatically active in metabolite extracts.Nature communications · 2024Article
- Demonstrating the reliability of in vivo metabolomics based chemical grouping: towards best practice.Archives of toxicology · 2024Article
- FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response.Briefings in bioinformatics · 2024Article
- VARIDT 3.0: the phenotypic and regulatory variability of drug transporter.Nucleic acids research · 2024Article
- TheMarker: a comprehensive database of therapeutic biomarkers.Nucleic acids research · 2024Article
- TTD: Therapeutic Target Database describing target druggability information.Nucleic acids research · 2024Article
- Metabolomics highlights biochemical perturbations occurring in the kidney and liver of mice administered a human dose of colistin.Frontiers in molecular biosciences · 2024Article
- Article
- RNAenrich: a web server for non-coding RNA enrichment.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A typical output of a metabolomic experiment is a peak table corresponding to the intensity of measured signals. Peak table processing, an essential procedure in metabolomics, is characterized by its study dependency and combinatorial diversity. While various methods and tools have been developed to facilitate metabolomic data processing, it is challenging to determine which processing workflow will give good performance for a specific metabolomic study. NOREVA, an out-of-the-box protocol, was therefore developed to meet this challenge. First, the peak table is subjected to many processing workflows that consist of three to five defined calculations in combinatorially determined sequences. Second, the results of each workflow are judged against objective performance criteria. Third, various benchmarks are analyzed to highlight the uniqueness of this newly developed protocol in (1) evaluating the processing performance based on multiple criteria, (2) optimizing data processing by scanning thousands of workflows, and (3) allowing data processing for time-course and multiclass metabolomics. This protocol is implemented in an R package for convenient accessibility and to protect users' data privacy. Preliminary experience in R language would facilitate the usage of this protocol, and the execution time may vary from several minutes to a couple of hours depending on the size of the analyzed data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.